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The AGAMOUS gene from Arabidopsis thaliana is required for organ identity, meristem determinacy, and maintenance of floral identity. The latter is spectacularly demonstrated in certain genetic combinations, such as the agamous LFY:VP16 plant shown in this drawing by Kirsten Bomblies (University of Wisconsin). Flowers revert to inflorescences that produce new lateral flowers with an indeterminate number of sepals and petals. Sequences that specify region-specific expression of AGAMOUS are located in one of the introns, and previous work has identified a small number of regulatory motifs by directly testing their interaction with candidate transcription factors. The study by Hong et al. (pages 1296-1309) reveals the potential as well as the limitations of the related approaches of phylogenetic footprinting and shadowing for identifying additional regulatory motifs using only sequence information.